Variant report

Variant	rs1539339
Chromosome Location	chr9:115593729-115593730
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:115586128..115587696-chr9:115592074..115593808,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10081751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11794056	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12555425	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes]
rs34627036	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3802493	0.90[CEU][hapmap];0.81[TSI][hapmap]
rs4978508	1.00[ASW][hapmap];0.90[CEU][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs4979149	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4979174	0.90[CEU][hapmap]
rs62576368	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758198	chr9:115240454-116002951	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759710	chr9:115240454-116002951	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv515899	chr9:115359049-115593870	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv2757350	chr9:115371397-115594108	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1038306	chr9:115379305-115595695	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv540194	chr9:115379305-115595695	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv430090	chr9:115383445-115594445	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv893733	chr9:115397206-115712068	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
9	esv2422302	chr9:115550339-115656433	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1539339	SLC46A2	cis	cerebellum	SCAN
rs1539339	PRPF4	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115552800-115593800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:115555800-115597400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr9:115559400-115598400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr9:115559600-115593800	Weak transcription	Brain Germinal Matrix	brain
5	chr9:115565000-115600800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr9:115565600-115600800	Weak transcription	HMEC	breast
7	chr9:115566800-115598000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr9:115569600-115593800	Weak transcription	Fetal Brain Female	brain
9	chr9:115570600-115608400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr9:115573000-115593800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr9:115573200-115593800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr9:115573200-115598400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr9:115573400-115595600	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr9:115573400-115598800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr9:115573600-115598400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr9:115573600-115607800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr9:115574000-115593800	Weak transcription	HepG2	liver
18	chr9:115574000-115598600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr9:115575000-115600800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr9:115577600-115630400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr9:115577800-115594000	Weak transcription	NH-A	brain
22	chr9:115578800-115596200	Weak transcription	Gastric	stomach
23	chr9:115579000-115600800	Weak transcription	Fetal Brain Male	brain
24	chr9:115580200-115608400	Weak transcription	Fetal Kidney	kidney
25	chr9:115580600-115601800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:115580800-115596400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr9:115581200-115598600	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr9:115581200-115599200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr9:115582200-115608600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr9:115582400-115593800	Weak transcription	Adipose Nuclei	Adipose
31	chr9:115582400-115593800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr9:115582400-115593800	Weak transcription	Fetal Muscle Trunk	muscle
33	chr9:115582400-115593800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr9:115582400-115598200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr9:115582400-115598400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr9:115582400-115600600	Weak transcription	HSMM	muscle
37	chr9:115582400-115608600	Weak transcription	NHLF	lung
38	chr9:115582400-115609000	Weak transcription	NHDF-Ad	bronchial
39	chr9:115582400-115630000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr9:115582600-115594200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr9:115582600-115598600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr9:115583200-115593800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr9:115583400-115598200	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr9:115583400-115598200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr9:115583600-115593800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr9:115583600-115593800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr9:115583600-115598400	Weak transcription	NHEK	skin
48	chr9:115584400-115608800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr9:115585000-115596000	Weak transcription	Brain Angular Gyrus	brain
50	chr9:115585200-115594200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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